Visualization of molecular flexibility and its effects on electrostatic recognition.
To study the effect of protein flexibility on electrostatic recognition, we have devised two novel computer graphic representations of the changes in the electrostatic field of a protein resulting from its internal motions. The atomic structure of Cu, Zn superoxide dismutase was minimized, and the 200 lowest frequency normal modes of the enzyme were determined. Individual and combined normal-mode vibrations were visualized interactively with the program Flex. Normal-mode motions are fast enough (approximately 10(-11) s cycle-1) to evade solvent damping, thus allowing long-range electrostatic interactions to dominate. The changing electrostatic environment of the protein was examined by animating precalculated frames of electrostatic field vectors with GRAMPS. With Vu, changes in electrostatic potential were displayed as variations in the color-coding of dots lying on a consensus surface that maintains the protein's shape. The consensus surface was calculated with the program Sphinx, and was derived from spherical harmonic approximations of expanded molecular surfaces. The ability to view the effects of molecular motions interactively should be useful in understanding the relationships of protein structure to function.
Fisher
C L
CL
Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.
Tainer
J A
JA
Pique
M E
ME
Getzoff
E D
ED
D003196:Computer Graphics; D004563:Electrochemistry; D008433:Mathematics; D008958:Models, Molecular; D009038:Motion; D011506:Proteins / Q000737:chemistry*; D013482:Superoxide Dismutase / Q000737:chemistry
D011506:Proteins; D013482:Superoxide Dismutase